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Updates sarek_subway #1653

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Updates sarek_subway #1653

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nevinwu
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@nevinwu nevinwu commented Sep 13, 2024 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

This PR updates the metro map for sarek (sarek_subway) with lofreq. Closes #1651

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github-actions bot commented Sep 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c1ccb9f

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-13 15:48:43

FriederikeHanssen
FriederikeHanssen reviewed Sep 13, 2024
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  • can you add this white padding on the side? SOrry didn't see that on slack. In inkscape i think it is under document properties -> resize to content and then something like add margin or so.

If it's not possible that's ok and @maxulysse or me can do it.

  • update the changelog

@nevinwu
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nevinwu commented Sep 13, 2024

I have noticed now what you mean by this white padding now that I see the "Files changed" here in GitHub. Sorry.

I have tried to, but I can't find that option I don't really know how to do it. Could you guys please do it? :)

On the other side, I have updated the CHANGELOG.

@FriederikeHanssen
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@maxulysse actions are failing because of outdated actions. Should we merge anyways since no code changes were done?

@nevinwu
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nevinwu commented Sep 13, 2024

What do you mean by "outdated actions"? I'm curious.

@maxulysse actions are failing because of outdated actions.

@FriederikeHanssen
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If you click on the 'Details' you can see the error messages of the failing ones and it says

Error: This request has been automatically failed because it uses a deprecated version of `actions/upload-artifact: v2`. Learn more: https://github.blog/changelog/2024-02-13-deprecation-notice-v1-and-v2-of-the-artifact-actions/

@maxulysse
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Can you save the whole page and not the drawing only when you export?

@nevinwu
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nevinwu commented Sep 13, 2024

I think that it is correct now.

@maxulysse
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@maxulysse actions are failing because of outdated actions. Should we merge anyways since no code changes were done?

WHAAT?

@maxulysse
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but yeah, let's merge anyway, that's a work for next week us

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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@nevinwu @FriederikeHanssen @maxulysse